GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruII-B in Malonomonas rubra DSM 5091

Align Phosphotransferase system IIB component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate WP_072908771.1 BUB13_RS10825 PTS fructose-like transporter subunit IIB

Query= TCDB::Q5V5X1
         (143 letters)



>NCBI__GCF_900142125.1:WP_072908771.1
          Length = 575

 Score =  108 bits (269), Expect = 2e-28
 Identities = 58/117 (49%), Positives = 80/117 (68%), Gaps = 1/117 (0%)

Query: 3   LVAVTSCPTGIAHSQMAAENLEQTAEEQGHDIKVEVQGAMGAENELSDSDIEAADAAIIA 62
           +V VTSCPTGIAH+ MAAE L++ AEE GH++K+E QG++GA+N LSD +I  ADA IIA
Sbjct: 118 IVGVTSCPTGIAHTFMAAEALKKAAEELGHEVKIETQGSVGAKNVLSDDEIARADAVIIA 177

Query: 63  SDTSVSQDRFSGVPLIDGTVKDAVNDAEGMIADAVKAADGDTP-ARETDVGSSEASA 118
           +D  V + RFSG PL + + K+A+++    I  A+ AA      A++ D   SE SA
Sbjct: 178 ADAFVDKTRFSGKPLFETSTKEALHNGANAIQAALSAAPAAKGLAKQVDDLKSERSA 234



 Score = 81.6 bits (200), Expect = 2e-20
 Identities = 41/99 (41%), Positives = 63/99 (63%)

Query: 2   KLVAVTSCPTGIAHSQMAAENLEQTAEEQGHDIKVEVQGAMGAENELSDSDIEAADAAII 61
           K+VAVT+CPTG+AH+ MAAE L++ A+  GH++++E QG+ GA++ L+   I  AD  II
Sbjct: 3   KIVAVTACPTGVAHTFMAAEALKKVADTMGHELELETQGSEGAKDVLAPDAIAQADVVII 62

Query: 62  ASDTSVSQDRFSGVPLIDGTVKDAVNDAEGMIADAVKAA 100
           A+D  V   RF+G  +   +  DA+   + +I  A   A
Sbjct: 63  AADIHVDPSRFAGKAIHAVSTSDAIRQTKEVIEAAFAEA 101


Lambda     K      H
   0.308    0.124    0.328 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 158
Number of extensions: 5
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 143
Length of database: 575
Length adjustment: 26
Effective length of query: 117
Effective length of database: 549
Effective search space:    64233
Effective search space used:    64233
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory